Britain has imposed a ban on entry visas for young Nigerians aged between 18 and 30 who intend to visit the UK for the first time.
About 80% of visa applications from Nigeria are refused, says the FO
The British High Commission in Nigeria says it cannot deal with the high number of visa applications, which have nearly doubled in the last two years.
The temporary ban will remain in force until next year, while the office is reorganised to improve visa service.
But an official at the Nigerian presidency said it was "very unfair".
"We enjoy a close relationship with the United Kingdom," said Femi Fani-Kayode, special assistant to the Nigerian president on public affairs
"I don't think this is the way to strengthen ties between the two countries."
The visa refusal rate is particularly high in Nigeria, where about 80% of applications from young people are turned down.
Some are rejected because they have forged documents, says the BBC's Anna Borzello in Lagos.
The UK Foreign Office said it will improve the service offered to applicants.
"We are going to look at how applications are currently processed and see if there are ways of making it more efficient," said a Foreign Office spokeswoman.
Those studying in the UK, or members of Business Express - a scheme for large companies with strong UK links - will not be affected.
And first-time visitors who are married to someone with proof they have travelled to Britain in the last five years can also still apply.
Cases will also be considered in a "genuine emergency or on urgent compassionate grounds", the Foreign Office said.
The British High Commission in the Nigerian capital, Abuja, and the Deputy High Commission in Lagos deal with 23,000 visa applications a month.
The spokeswoman said the Foreign Office did not want to stop all applications and welcomed Nigerians to the UK.
But she added: "First-time visitors, particularly within that age group [18 to 30], are particularly time-consuming, each has to be interviewed and obviously an intention to return has to be verified."
Keith Best, chief executive of the Immigration Advisory Service, a charity which advises immigrants, said they were considering opening an office in Lagos to assist the local population.
He said he had opposed similar restrictions on working holiday visas for people in Pakistan and thought the temporary ban in Nigeria was "entirely wrong".
"If you open an immigration category then people should have access to it. It's not their fault if there are inefficiencies in the system and [officials] can't deal with it," he said.
Sir Andrew Green, chairman of Migrationwatch UK, said the decision to delay visa applications was "without precedent."
"The government's policy - or lack of it - has triggered enormous pressure on our visa issuing posts. Demand for visas has risen by a third in the last five years to reach roughly two million a year.
"The Public Accounts Committee found recently that one in five posts could no longer cope with daily demand for visas."